Predict gene knockout strategies¶

In cameo we have two ways of predicting gene knockout targets: using evolutionary algorithms (OptGene) or linear programming (OptKnock)

from cameo import models

model = models.bigg.iJO1366
model.solver = "cplex"
wt_solution = model.solve()
growth = wt_solution.fluxes["BIOMASS_Ec_iJO1366_core_53p95M"]
acetate_production = wt_solution.fluxes["EX_succ_e"]

from cameo import phenotypic_phase_plane

p = phenotypic_phase_plane(model, variables=['BIOMASS_Ec_iJO1366_core_53p95M'], objective='EX_succ_e')
p.plot(height=300, points=[(growth, acetate_production)])

OptGene¶

OptGene is an approach to search for gene or reaction knockouts that relies on evolutionary algorithms[1]. The following image from authors summarizes the OptGene workflow.

Every iteration we keep the best 50 individuals so we can generate a library of targets.

from cameo.strain_design.heuristic.evolutionary_based import OptGene

optgene = OptGene(model)

result = optgene.run(target="succ_e",
                     biomass="BIOMASS_Ec_iJO1366_core_53p95M",
                     substrate="glc__D_e",
                     max_evaluations=50000,
                     robust=False)

Starting optimization at Thu, 14 Jan 2016 15:47:30

Using saved session configuration for http://localhost:5006/
To override, pass 'load_from_config=False' to Session

/Users/joao/.virtualenvs/cameo-py3/lib/python3.4/site-packages/bokeh/session.py:318 [1;31mUserWarning[0m: You need to start the bokeh-server to see this example.

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Finished after 00:50:42

result._processed_solutions

OptKnock¶

OptKnock uses a bi-level mixed integer linear programming approach to identify reaction knockouts[2]:

\[\begin{split}\begin{matrix} maximize & \mathit{v_{chemical}} & & (\mathbf{OptKnock}) \\ \mathit{y_j} & & & \\ subject~to & maximize & \mathit{v_{biomass}} & (\mathbf{Primal}) \\ & \mathit{v_j} & & & & \\ \end{matrix}\\ \begin{bmatrix} subject~to & \sum_{j=1}^{M}S_{ij}v_{j} = 0,\\ & v_{carbon\_uptake} = v_{carbon~target}\\ & v_{apt} \ge v_{apt\_main}\\ & v_{biomass} \ge v_{target_biomass}\\ & v_{j}^{min} \cdot y_j \le v_j \le v_{j}^{max} \cdot y_j, \forall j \in \boldsymbol{M} \\ \end{bmatrix}\\ \begin{align} & y_j = {0, 1}, & & \forall j \in \boldsymbol{M} & \\ & \sum_{j \in M} (1 - y_j) \le K& & & \\ \end{align}\end{split}\]

from cameo.strain_design.deterministic.linear_programming import OptKnock

optknock = OptKnock(model)

Warning:  File contains basis.  Basis is loaded.

result = optknock.run(max_knockouts=2, target="EX_succ_e", biomass="BIOMASS_Ec_iJO1366_core_53p95M", max_results=2)

---------------------------------------------------------------------------

TypeError                                 Traceback (most recent call last)

<ipython-input-11-277898a50993> in <module>()
----> 1 result = optknock.run(max_knockouts=2, target="EX_succ_e", biomass="BIOMASS_Ec_iJO1366_core_53p95M", max_results=2)


/Users/joao/Documents/repos/cameo/cameo/strain_design/deterministic/linear_programming.py in run(self, max_knockouts, biomass, target, max_results, *args, **kwargs)
    234                 fluxes_list.append(solution.fluxes)
    235                 production_list.append(solution.f)
--> 236                 biomass_list.append(solution[biomass])
    237
    238                 # Add an integer cut


TypeError: 'LazySolution' object is not subscriptable

result

result.plot(1)

References¶

[1]Patil, K. R., Rocha, I., Förster, J., & Nielsen, J. (2005). Evolutionary programming as a platform for in silico metabolic engineering. BMC Bioinformatics, 6, 308. doi:10.1186/1471-2105-6-308

[2]Burgard, A.P., Pharkya, P., Maranas, C.D. (2003), “OptKnock: A Bilevel Programming Framework for Identifying Gene Knockout Strategies for Microbial Strain Optimization,” Biotechnology and Bioengineering, 84(6), 647-657.

Predict gene knockout strategies¶

OptGene¶

OptKnock¶

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